A lot of people tend to go with Bakflip. They are really low profile and make a good quality product. The price is definitely a little higher too though. I have a Peragon cover on my truck and I love it. Does exactly what I need it to and is still low profile. I love how you can take it right out of the truck too and have access to the full bed with no cover blocking your rear window. The pictures I took when I put it on are kind of bad quality...
Open cover (can be fully removed from the truck as well in about 30 seconds.
Here's a link to their website: http://peragon.com/
You'll find some better pictures there and a few videos on how they work and such.